SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant-of-concern has rapidly spread across the globe to become the dominant form of COVID-19 infection. The Omicron Spike (S) glycoprotein, which mediates viral entry into cells, possesses up to 34 mutations that contribute to the variant's increased transmissibility and decreased susceptibility to antibody-mediated immunity from vaccines or prior infections. One of those mutations, Q954H, occurs within the N-terminal heptad repeat (HR1) domain. During viral entry, the HR1 domain coassembles with the C-terminal heptad repeat (HR2) domain to form a stable six-helix bundle or "fusion core" structure, which brings the viral envelope and host membrane into proximity and thermodynamically drives membrane fusion. Here, we demonstrate that the Q954H mutation enhances the interaction between the HR1 and HR2 domains, thereby stabilizing the fusion core assembly relative to prior variants. We also report the first X-ray crystal structure of the Omicron S fusion core, which reveals that the Q954H side chain forms a N···H-O hydrogen bond with the side chain hydroxyl of S1175 within the HR2 domain, as well as an unexpected C-H···O hydrogen bonding interaction with the backbone carbonyl of N1173. Co-assembly with a synthetic depsipeptide, in which the amide of N1173 is replaced with an ester, results in a decreased assembly stability, providing evidence to support the importance of the observed hydrogen bond network. These insights will be valuable for analyzing the factors that drive viral evolution and for the development of inhibitors of SARS-CoV-2 entry.